Contacts of the strand formed by residues 162 - 169 (chain A) in PDB entry 6N8P


Residue contacts within the protein are derived with the CSU software (Sobolev V., Sorokine A., Prilusky J., Abola E.E. and Edelman M. (1999) Automated analysis of interatomic contacts in proteins. Bioinformatics, 15, 327-332). A short description of the analytical approach is given at the end of the page.
For CSU analysis of other PDB entry

Note:
Non-standard 3 letter residue codes indicate a heterogroup. To identify and analyse, use LPC software

Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB   - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC   - hydrophobic-hydrophilic contact (destabilizing contact)
+/-  - indicates presence/absence of a specific contacts
*    - indicates residues forming contacts  by their side chain
       (including CA atoms)
Residues in contact with ARG 162 (chain A).
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    156A  VAL*     4.7     0.2    -      -       -      -
    157A  GLN*     3.3    29.9    +      -       +      +
    160A  ALA*     3.3    10.7    -      -       +      +
    161A  PHE*     1.3    73.2    -      -       -      +
    163A  ALA*     1.3    60.8    +      -       -      +
    164A  LEU*     2.9    26.0    +      -       +      +
----------------------------------------------------------
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Residues in contact with ALA 163 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    117A  PHE*     3.9    28.0    -      -       +      -
    119A  LEU*     4.9     6.7    -      -       +      -
    154A  PHE*     6.2     2.5    -      -       +      -
    155A  VAL      3.7     8.1    -      -       -      +
    156A  VAL*     4.3     9.0    -      -       +      -
    161A  PHE      3.4     6.1    +      -       -      -
    162A  ARG*     1.3    67.3    -      -       -      +
    164A  LEU*     1.3    60.6    +      -       -      +
    165A  GLU*     3.0    32.0    +      -       -      +
----------------------------------------------------------
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Residues in contact with LEU 164 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     4.2     9.2    -      -       +      -
    155A  VAL*     2.9    20.4    +      -       +      +
    157A  GLN*     3.8    35.2    -      -       +      +
    162A  ARG*     2.9    32.2    +      -       +      +
    163A  ALA*     1.3    67.4    -      -       -      +
    165A  GLU*     1.3    62.7    +      -       -      +
    166A  ASP*     3.1     8.5    +      -       +      +
    167A  ARG*     3.4    48.7    +      -       +      +
    168A  THR*     3.6     9.0    +      -       -      -
----------------------------------------------------------
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Residues in contact with GLU 165 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    154A  PHE*     4.6    12.6    -      -       -      -
    163A  ALA*     3.0    24.6    +      -       -      +
    164A  LEU*     1.3    71.9    -      -       -      +
    166A  ASP*     1.3    61.7    +      -       -      +
    167A  ARG      3.4     0.2    -      -       -      -
    168A  THR*     3.5    23.9    +      -       -      -
----------------------------------------------------------
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Residues in contact with ASP 166 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    164A  LEU*     3.1     4.4    -      -       +      -
    165A  GLU*     1.3    80.3    -      -       -      +
    167A  ARG*     1.3    69.6    +      -       +      +
    168A  THR      3.3     4.1    +      -       -      +
----------------------------------------------------------
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Residues in contact with ARG 167 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    143A  LEU*     3.9    22.6    -      -       -      +
    145A  TYR*     5.0     3.4    +      -       -      -
    155A  VAL*     3.3    40.7    -      -       +      +
    164A  LEU*     3.4    35.8    +      -       +      +
    166A  ASP*     1.3    86.2    -      -       +      +
    168A  THR*     1.3    64.5    +      -       -      +
    169A  ILE*     3.4     9.7    +      -       -      +
    218A  LEU*     6.1     0.2    -      -       -      +
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Residues in contact with THR 168 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    152A  ASN*     4.9     2.5    -      -       +      -
    153A  VAL      3.6     9.9    -      -       -      +
    154A  PHE*     3.5    46.1    -      -       +      +
    155A  VAL*     4.8     0.2    -      -       -      -
    164A  LEU      3.6     9.8    +      -       -      -
    165A  GLU*     3.5    21.8    +      -       -      -
    166A  ASP      3.3     5.4    -      -       -      +
    167A  ARG*     1.3    77.1    -      -       -      +
    169A  ILE*     1.3    69.7    +      -       -      +
    170A  SER*     3.6    10.8    +      -       -      +
    173A  ALA*     5.9     0.2    -      -       -      +
----------------------------------------------------------
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Residues in contact with ILE 169 (chain A). Click here for Legend to table.
----------------------------------------------------------
                                  Specific contacts
                               ---------------------------
     Residue       Dist    Surf   HB    Arom    Phob    DC
----------------------------------------------------------
    145A  TYR*     4.7     5.2    -      -       +      -
    151A  GLY      4.4     1.0    -      -       -      +
    152A  ASN*     3.5     0.9    -      -       -      -
    153A  VAL*     2.9    46.1    +      -       +      +
    155A  VAL*     5.3     0.2    -      -       +      -
    167A  ARG      3.7    13.0    -      -       -      +
    168A  THR*     1.3    71.4    -      -       -      +
    170A  SER*     1.3    62.3    +      -       -      +
    173A  ALA*     5.4     1.3    -      -       +      -
    174A  VAL*     3.7    27.1    -      -       +      -
    204A  ILE*     3.8    23.8    -      -       +      -
    206A  ILE*     4.1    12.8    -      -       +      -
    208A  TYR*     5.7     0.2    +      -       -      -
    216A  TRP*     3.6    46.7    -      -       +      +
    218A  LEU*     3.8     9.6    -      -       +      -
----------------------------------------------------------
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A short description of the analytical approach
The contact analysis used in this page is based upon the approach developed in: Sobolev V., Wade R.C., Vriend G. and Edelman M. PROTEINS (1996) 25, 120-129. Contact legitimacy depends on the hydrophobic-hydrophilic properties of the contacting atoms. In order to define it, for each inter-atomic contact, eight atom classes have been introduced:


   I  Hydrophilic      - N and O that can donate and accept hydrogen bonds
                         (e.g., oxygen of hydroxyl group of Ser. or Thr)
  II  Acceptor         - N or O that can only accept a hydrogen bond
 III  Donor            - N that can only donate a hydrogen bond
  IV  Hydrophobic      - Cl, Br, I and all C atoms that are not in
                         aromatic rings and do not have a covalent bond to
                         a N or O atom
   V  Aromatic         - C in aromatic rings irrespective of any other 
                         bonds formed by the atom
  VI  Neutral          - C atoms that have a covalent bond to at least one
                         atom of class I or two or more atoms from class II
                         or III; atoms; S, F, P, and metal atoms in all cases
 VII  Neutral-donor    - C atoms that have a covalent bond with only one
                         atom of class III
VIII  Neutral-acceptor - C atoms that have a covalent bond with only 
                         one atom of class II
For each pair of contacts the state of legitimacy is shown below:

Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
  Atomic class           I  II  III   IV   V   VI  VII  VIII
------------------------------------------------------------
   I  (Hydrophilic)      +   +    +    -   +   +    +    +
  II  (Acceptor)         +   -    +    -   +   +    +    -
 III  (Donor)            +   +    -    -   +   +    -    +
  IV  (Hydrophobic)      -   -    -    +   +   +    +    +
   V  (Aromatic)         +   +    +    +   +   +    +    +
  VI  (Neutral)          +   +    +    +   +   +    +    +
 VII  (Neutral-donor)    +   +    -    +   +   +    -    +
VIII  (Neutral-acceptor) +   -    +    +   +   +    +    -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically assigned based on the atomic coordinates. However, in three cases (see below) the automatic assignment is currently ambiguous. In these cases, the user is advised to manually analyse the full list of contacts using LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are 
   considered "aromatic" (Class V) if the ring is approximately
   planar, and "hydrophobic" (Class IV) or "neutral" (Classes
   VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
   "hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
   "carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).

Please E-mail any questions and/or suggestions concerning this page to Vladimir.Sobolev@weizmann.ac.il